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Detailed information for vg0335272611:

Variant ID: vg0335272611 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 35272611
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, T: 0.02, others allele: 0.00, population size: 115. )

Flanking Sequence (100 bp) in Reference Genome:

TCGAACACCATGATGCCTGACGCATTCACGATTGAGCGAACATAAAGTCATGCTTAATATTATCATTTTTTTTCTTGGGATAGCCTAACTAACATTGACA[T/A]
AAAAATCCTAAAAATATCAAGTATAATTACAATATAACTAGTACGTAGTATATAATTATAATAGCATAAGTTATAAGCAACTATATAAACCCGCGGCAGC

Reverse complement sequence

GCTGCCGCGGGTTTATATAGTTGCTTATAACTTATGCTATTATAATTATATACTACGTACTAGTTATATTGTAATTATACTTGATATTTTTAGGATTTTT[A/T]
TGTCAATGTTAGTTAGGCTATCCCAAGAAAAAAAATGATAATATTAAGCATGACTTTATGTTCGCTCAATCGTGAATGCGTCAGGCATCATGGTGTTCGA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	55.00%	44.80%	0.23%	0.00%	NA
All Indica	2759	28.30%	71.30%	0.36%	0.00%	NA
All Japonica	1512	99.10%	0.90%	0.07%	0.00%	NA
Aus	269	65.40%	34.60%	0.00%	0.00%	NA
Indica I	595	35.80%	63.20%	1.01%	0.00%	NA
Indica II	465	12.00%	88.00%	0.00%	0.00%	NA
Indica III	913	32.50%	67.10%	0.33%	0.00%	NA
Indica Intermediate	786	27.50%	72.40%	0.13%	0.00%	NA
Temperate Japonica	767	99.00%	0.90%	0.13%	0.00%	NA
Tropical Japonica	504	98.80%	1.20%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	52.20%	47.80%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0335272611	T -> A	LOC_Os03g62270.1	downstream_gene_variant ; 2862.0bp to feature; MODIFIER	silent_mutation	Average:67.812; most accessible tissue: Minghui63 flower, score: 83.835	N	N	N	N
vg0335272611	T -> A	LOC_Os03g62270-LOC_Os03g62280	intergenic_region ; MODIFIER	silent_mutation	Average:67.812; most accessible tissue: Minghui63 flower, score: 83.835	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0335272611	NA	8.51E-13	mr1503	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0335272611	NA	2.77E-21	mr1627_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0335272611	NA	1.70E-06	mr1928_2	Ind_All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251